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Magnesium in PDB 3zgz: Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation

Enzymatic activity of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation

All present enzymatic activity of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation:
6.1.1.4;

Protein crystallography data

The structure of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation, PDB code: 3zgz was solved by S.Chopra, A.Palencia, C.Virus, A.Tripathy, B.R.Temple, A.Velazquez-Campoy, S.Cusack, J.S.Reader, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.59 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.580, 68.190, 226.220, 90.00, 105.53, 90.00
R / Rfree (%) 18.681 / 23.822

Other elements in 3zgz:

The structure of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation (pdb code 3zgz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation, PDB code: 3zgz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3zgz

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Magnesium binding site 1 out of 7 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1077

b:32.9
occ:1.00
 O B:HOH2058 2.2 36.3 1.0
O B:HOH2061 2.2 34.8 1.0
O B:HOH2060 2.2 37.0 1.0
O B:HOH2062 2.2 34.8 1.0
O B:HOH2059 2.2 35.4 1.0
OP2 B:U20 2.3 37.4 1.0
P B:U20 3.6 38.0 1.0
O4 B:U60 3.9 37.1 1.0
N7 B:G59 4.0 31.6 1.0
OP1 B:U20 4.1 36.0 1.0
OP2 B:G59 4.3 29.7 1.0
O4 B:U48 4.3 26.6 1.0
O5' B:U20 4.4 36.9 1.0
O4' B:A20A 4.4 29.1 1.0
C4' B:G19 4.7 35.6 1.0
C5' B:U20 4.7 36.1 1.0
O5' B:A20A 4.7 31.4 1.0
C8 B:G59 4.7 31.8 1.0
OP1 B:A20A 4.8 34.1 1.0
O3' B:G19 4.8 37.2 1.0
C3' B:U20 4.9 33.8 1.0
C4 B:U60 4.9 35.7 1.0
C2 B:A15 5.0 28.6 1.0
C5' B:G19 5.0 35.9 1.0

Magnesium binding site 2 out of 7 in 3zgz

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Magnesium binding site 2 out of 7 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1078

b:62.3
occ:1.00
 O B:HOH2064 2.2 65.2 1.0
O B:HOH2066 2.2 66.2 1.0
O B:HOH2063 2.2 55.9 1.0
O B:HOH2065 2.2 62.8 1.0
N7 B:G45 2.6 44.2 1.0
O6 B:G45 3.1 46.1 1.0
C5 B:G45 3.4 45.0 1.0
C6 B:G45 3.6 44.3 1.0
C8 B:G45 3.7 45.6 1.0
O B:HOH2031 4.2 29.6 1.0
O6 B:G46 4.2 47.5 1.0
N2 B:G47J 4.3 36.4 1.0
C4 B:G45 4.7 44.5 1.0
N7 B:G46 4.7 45.2 1.0
OP1 B:G45 4.7 63.0 1.0
C2 B:G47J 4.8 36.0 1.0
N9 B:G45 4.8 45.5 1.0
N1 B:G47J 4.9 35.9 1.0
C6 B:G46 4.9 46.6 1.0
N1 B:G45 4.9 44.1 1.0

Magnesium binding site 3 out of 7 in 3zgz

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Magnesium binding site 3 out of 7 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1079

b:44.0
occ:1.00
 OP2 B:G9 1.8 24.7 1.0
OP2 B:U8 1.8 25.9 1.0
O B:HOH2068 2.2 45.8 1.0
O B:HOH2069 2.2 39.7 1.0
O B:HOH2067 2.2 44.6 1.0
O B:HOH2070 2.2 47.6 1.0
P B:U8 3.2 26.5 1.0
P B:G9 3.3 26.1 1.0
O5' B:U8 3.7 24.9 1.0
O B:HOH2073 3.8 40.1 1.0
C5' B:U8 4.1 24.7 1.0
OP1 B:G9 4.1 27.6 1.0
O3' B:A7 4.1 25.5 1.0
O5' B:G9 4.1 27.0 1.0
O B:HOH2013 4.2 25.1 1.0
O3' B:U8 4.2 25.8 1.0
OP1 B:U8 4.2 24.4 1.0
C5' B:G9 4.3 27.5 1.0
C3' B:U8 4.4 24.7 1.0
O B:HOH2019 4.6 40.5 1.0
OP1 B:U11 4.7 35.4 1.0
O B:HOH2017 4.8 26.8 1.0
C4' B:U8 4.8 24.6 1.0
O B:HOH2072 4.9 37.1 1.0
MG B:MG1080 5.0 41.3 1.0

Magnesium binding site 4 out of 7 in 3zgz

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Magnesium binding site 4 out of 7 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1080

b:41.3
occ:1.00
 OP1 B:U8 2.0 24.4 1.0
O B:HOH2074 2.2 43.0 1.0
O B:HOH2071 2.2 42.6 1.0
O B:HOH2073 2.2 40.1 1.0
O B:HOH2072 2.2 37.1 1.0
O B:HOH2075 2.2 35.9 1.0
P B:U8 3.3 26.5 1.0
OP2 B:G13 3.6 26.5 1.0
OP2 B:U8 3.7 25.9 1.0
O B:HOH2070 4.0 47.6 1.0
OP2 B:G12 4.0 28.8 1.0
OP1 B:G12 4.1 29.3 1.0
O5' B:U8 4.3 24.9 1.0
O3' B:A7 4.3 25.5 1.0
C4' B:A7 4.4 24.9 1.0
O B:HOH2012 4.4 30.8 1.0
P B:G12 4.5 28.9 1.0
C3' B:A7 4.7 24.9 1.0
C5' B:A7 4.7 23.9 1.0
O B:HOH2068 4.8 45.8 1.0
P B:G13 4.8 26.0 1.0
C5 B:U8 4.9 22.4 1.0
N7 B:G13 4.9 22.9 1.0
MG B:MG1079 5.0 44.0 1.0
O5' B:G12 5.0 27.6 1.0

Magnesium binding site 5 out of 7 in 3zgz

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Magnesium binding site 5 out of 7 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1081

b:55.2
occ:1.00
 OP1 B:C50 2.0 34.5 1.0
O B:HOH2039 2.5 24.7 1.0
OP1 B:U48 2.5 37.1 1.0
P B:C50 3.4 35.7 1.0
P B:U48 3.9 36.4 1.0
O5' B:C50 4.1 36.4 1.0
O B:HOH2040 4.1 33.2 1.0
OP2 B:C50 4.3 37.0 1.0
O5' B:G49 4.4 29.7 1.0
O3' B:G49 4.5 35.2 1.0
C3' B:U48 4.5 28.9 1.0
O5' B:U48 4.5 34.5 1.0
OP2 B:G49 4.6 29.6 1.0
OP1 B:G51 4.6 36.0 1.0
OP2 B:U48 4.6 37.8 1.0
C3' B:G49 4.8 34.0 1.0
C5 B:C50 4.8 33.0 1.0
O3' B:G47J 4.9 36.9 1.0
C5' B:U48 4.9 32.5 1.0

Magnesium binding site 6 out of 7 in 3zgz

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Magnesium binding site 6 out of 7 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1077

b:60.8
occ:1.00
 OP2 E:G9 2.1 58.8 1.0
OP2 E:U8 2.2 58.7 1.0
P E:U8 3.5 57.3 1.0
P E:G9 3.5 60.3 1.0
OP1 E:U8 4.1 55.9 1.0
OP2 E:U11 4.2 58.8 1.0
OP1 E:U11 4.2 59.0 1.0
OP1 E:G9 4.3 62.3 1.0
O5' E:G9 4.3 59.7 1.0
C5' E:G9 4.4 60.0 1.0
O5' E:U8 4.4 57.2 1.0
O3' E:U8 4.5 60.0 1.0
O3' E:A7 4.6 58.8 1.0
OP2 E:G12 4.6 51.8 1.0
P E:U11 4.8 59.3 1.0
C3' E:U8 4.8 58.8 1.0
C5' E:U8 4.9 58.9 1.0

Magnesium binding site 7 out of 7 in 3zgz

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Magnesium binding site 7 out of 7 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and Toxic Moiety From Agrocin 84 (TM84) in Aminoacylation- Like Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1078

b:59.2
occ:1.00
 OP1 E:U8 2.5 55.9 1.0
OP2 E:G13 2.9 47.4 1.0
P E:U8 4.0 57.3 1.0
C5 E:U8 4.1 52.9 1.0
P E:G13 4.3 46.4 1.0
N7 E:G13 4.3 48.8 1.0
C5' E:A7 4.4 56.9 1.0
O5' E:U8 4.4 57.2 1.0
C8 E:G13 4.4 47.7 1.0
C4' E:A7 4.6 57.9 1.0
C6 E:U8 4.6 54.6 1.0
O3' E:A7 4.8 58.8 1.0
OP1 E:G13 4.9 45.9 1.0
C3' E:A7 4.9 58.6 1.0
OP2 E:G12 4.9 51.8 1.0

Reference:

S.Chopra, A.Palencia, C.Virus, A.Tripathy, B.R.Temple, A.Velazquez-Campoy, S.Cusack, J.S.Reader. Plant Tumour Biocontrol Agent Employs A Trna-Dependent Mechanism to Inhibit Leucyl-Trna Synthetase Nat.Commun. V. 4 1417 2013.
ISSN: ISSN 2041-1723
PubMed: 23361008
DOI: 10.1038/NCOMMS2421
Page generated: Thu Aug 15 13:53:08 2024

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